# Fragment Analysis in R

## Documentation for package ‘Fragman’ version 1.0.9

- DESCRIPTION file.

## Help Pages

arrange.jm | Arrange data converted to joinmap code into a joinmap readable file
best.layout | complementary tools for layout
big.peaks.col | Peak search by first derivatives
detect.ladder | Ladder detection by correlation or confidence intervals
find.ladder | Ladder detection by correlation or confidence intervals
Fragman | Fragment analysis and automatic scoring
get.scores | complementary tools
homo.panel | complementary tools
homogenize.to.parentals | complementary tools
jm.conv | Scores to JoinMap converter
ladder.corrector | Ladder corrector attached to R environment
ladder.info.attach | Ladder detection and attachment to R environment
lapply_pb | complementary tools for Fragman
letter.to.jm | Letter to JoinMap code converter
my.plants | Cranberry biparental population
num.to.lett | Number to Letter code converter
overview | Assesing several plants with an overview
overview2 | Assesing several plants with an overview
plot.fsa_stored | plot form fsa files stored with storing.inds
pullup | Applying pullup to channels/colors
read.abif | Read ABIF formatted files
reals | Finding the real peaks
saturate | Checking and correcting saturated peaks
score.markers | Fragment analysis scoring
separate | Separating peaks by a shift window
storing.inds | Extracting channel information
threshs | Customizing thresholds
transfft | Applying the fourier transformation to a data frame
transp | Creating color with transparency